If you're starting from scratch first thing you do is setup your wheelbase which is 101.1" if I remember right. Have your lcas and torque arm in and adjust each side to proper wheelbase by adjusting your lcas.

Next comes the panhard hard adjustment to make sure the rear end is centered. But still check wheelbase after your panhard bar adjustment.

Next set set your ride height how you want it.... but you still need to keep your wheelbase checked if you're going low.

Then lastly set your pinion angle angle and your lca angle.

Be patient. Take your time. Check and recheck the measurements.

I pulled out my stock rear tear end last year and replaced it with an S60 along with bmr double adjustable everything with Viking coilovers. I spent a lot of time making sure my measurements were right and rechecked it. I was 1/32" off the wheelbase according to my measurements. I also did the front end as well. When I took it to an alignment shop the mechanic showed me I hit the wheelbase base and centering of the rear end perfectly. He only had to adjust the caster and camber up front.

Adjust your lcas for wheelbase not the torque arm. Your lcas will fight your torque arm and won't move your rear end. Adjust the lcas and the torque arm will just slide fwd or back in its bushing up at the front mounting point.